A BED file with targeted restriction enzyme fragment coordinates and the associated name of the primer used to target each fragment. Additional fields can be included with RE fragment characterstics (such as GC content) in columns after the strand column. Including additional features requires a header with the name of each feature.

Display the help message and command/subcommand options and arguments and exit.

-q, --quiet

Suppress all messages generated during HiFive processing.

5C Fend Options:

-r, --re str

The name of the restriction enzyme.

-g, --genome str

The name of the genome.

5C Data Options:

-B, --bam FILES

A pair of BAM filenames separated by spaces corresponding to the two independently-mapped ends of a set of reads. Multiple file pairs may be passed by calling this argument more than once. This option is mutually exclusive with -C/–count.

-C, --count FILE

A tabular text file containing pairs of fragment primer names and their associated read count (see Loading 5C Data for more information). This option is mutually exclusive with -B/–bam.

5C Project Options:

-f, --min-interactions int

The minimum number of interactions with valid fragments to keep a fragment in the analysis. [20]

-m, --min-distance int

The minimum distance between fragment midpoints to include in calculating numbers of interactions for fragment filtering and (if called by 5c-normalization or 5c-complete) the minimum interaction distance included in learning correction parameter values. [0]

-x, --max-distance int

The maximum distance between fragment midpoints to include in calculating numbers of interactions for fragment filtering and (if called by 5c-normalization or 5c-complete) the maximum interaction distance included in learning correction parameter values. A value of zero indicates no maximum distance cutoff. [0]

5C Normalization Options:

-r, --regions str

A comma-separated list of region numbers to include fragments from when calculating correction parameter values. [all regions]

-o, --output FILE

An optional filename to save the updated HiFive project to, leaving the original unchanged. [None]

5C Complete Options:

-o, --output FILES

A set of three filenames separated by spaces to save the newly-created HiFive fragment, dataset, and project files to. Mutually exclusive with -P/–prefix.

-P, --prefix str

A prefix for the output filenames. The file extensions .frags, .fcd, and .fcp will be used for the fragment, dataset, and project files, respectively. This option is mutually exclusive with -o/–output.

The maximum number of iterations to run the learning process for. [1000]

-t, --learning-threshold dec

The maximum change in log-likelihood necessary to stop the learning process early. [1.0]

-y, --binning-reads str

Which set of reads to use for learning correction parameter values, cis, trans, or all. [cis]

-v, --model str

A comma-separated list of fragment features to calculate corrections for. Acceptable features are len (length) and any features loaded in the BED file used to create the HiFive fragment file. [len]

-n, --model-bins str

A comma-separated list of numbers of bins to partition fragment features into for modeling. [10]

-u, --parameter-types str

A comma-separated list of model parameter types. Acceptable values are even, fixed, even-const, and fixed-const. Even means that fragment features are partitioned such that each bin has approximately even numbers of fragments. Fixed means that the range of the feature is divided into fixed-width bins. The -const suffix indicates that the correction values are held at their seed-values and not updated. [even]

If data is unbinned, this option specifies whether the heatmaps should be full or compact. Full means that there is a row and column for every fragment, while compact means that rows are forward fragments only and columns are reverse fragments only. [full]

-y, --dynamically-bin

Dynamically bin heatmap.

-x, --expansion-binsize int

The size of bins, in base pairs, to group data into for expanding under-populated bins. [10000]

-f, --minobservations int

The minimum number of observed reads in a bin for it to be considered valid. [20]

-g, --search-distance int

The furthest distance from the bin minpoint to expand bounds. If set to zero, there is no limit on expansion distance. [0]

-v, --remove-failed

If a non-zero ‘search-distance’ is given, it is possible for a bin not to meet the ‘minobservations’ criteria before stopping looking. If this occurs and ‘remove-failed’ is set, the observed and expected values for that bin are zero.

5C Interval Options:

-c, --region int

The index of the region to pull data from.

-b, --binsize int

The width of bins (in basepairs) to partition data into. A value of zero indicates that each bin is to correspond with a single fragment.

-s, --start int

The first coordinate of the region to pull data from. None indicates the beginning of the region. [None]

-e, --stop int

The last coordinate + 1 of the region to pull data from. None indicates the end of the region. [None]

-y, --dynamically-bin

Dynamically bin heatmap.

-x, --expansion-binsize int

The size of bins, in base pairs, to group data into for expanding under-populated bins. [10000]

-f, --minobservations int

The minimum number of observed reads in a bin for it to be considered valid. [20]

-g, --search-distance int

The furthest distance from the bin minpoint to expand bounds. If set to zero, there is no limit on expansion distance. [0]

-v, --remove-failed

If a non-zero ‘search-distance’ is given, it is possible for a bin not to meet the ‘minobservations’ criteria before stopping looking. If this occurs and ‘remove-failed’ is set, the observed and expected values for that bin are zero.

5C Plotting Options:

-i, --image FILE

Generate an image from the region or regions for which heatmap data is being calculated. [None]

-p, --pdf

Format the image as a pdf. [None]

-r, --rotate

Rotate the image 45 degrees so the chromosome axis is horizontal and only plot the triangle above this axis. This option can only be used with a full arraytype.

-t, --ticks

Add coordinate ticks and labels to heatmap. This option can only be used if a pdf is requested.

-l, --legend

Add a color scale bar corresponding to interaction strength. This option can only be used if a pdf is requested.

-n, --names

Add region names to the plot. This option can only be used if a pdf is requested.

-k, --keyword str

Pass additional plotting options accepted by the plotting module. Arguments should be of the format KEYWORD=VALUE. This option can be passed multiple times. [None]

Display the help message and command/subcommand options and arguments and exit.

-q, --quiet

Suppress all messages generated during HiFive processing.

HiC Fend Options:

-F, --fend FILE

A tabular file in a format compatible with HiCPipe containing fragment and fend indices, fragment length, start or end position, and any additional fragment features desired (see Loading HiC Fends for more information).

-B, --bed FILE

A BED file containing either restriction enzyme fragment coordinates or retriction enzyme cutsite coordinates. Fragment features may be included in columns after the strand column. Features should be formatted with one feature per column and two values per feature separated by a comma. If the coordinates are of RE fragment boundaries, the feature values should correspond to the upstream end of the fragment followed by the downstream end of the fragment. If the coordinates are of RE cutsites, the values should correspond to the sequence just upstream of the cutsite followed by the sequence just downstream of the cutsite. If additional features are included, the bed file must have a header line identifying the features.

-L, --length FILE

A tab-separated text file containing chromosome names and lengths. Must be used in conjunction with a positive value of ‘binned’.

--binned int

Indicates what size bins to break genome into. If None is passed, fend-level resolution is kept.

-r, --re str

The name of the restriction enzyme.

-g, --genome str

The name of the genome.

HiC Data Options:

-S, --bam FILES

A pair of BAM filenames separated by spaces corresponding to the two independently-mapped ends of a set of reads. Multiple file pairs may be passed by calling this argument more than once. This option is mutually exclusive with -R/–raw and -M/–mat.

The minimum number of interactions with valid fends to keep a fend in the analysis. [20]

-m, --min-distance int

The minimum distance between fend midpoints to include in calculating numbers of interactions for fend filtering and (if called by hic-normalization or hic-complete) the minimum interaction distance included in learning correction parameter values. [0]

-x, --max-distance int

The maximum distance between fend midpoints to include in calculating numbers of interactions for fend filtering and (if called by hic-normalization or hic-complete) the maximum interaction distance included in learning correction parameter values. A value of zero indicates no maximum distance cutoff. [0]

The number of bins to partition the interaction size ranges into for estimating the distance dependence function (see HiC Distance Dependence Estimation for more information). A value of zero indicates that finding the distance dependence function should be skipped.

HiC Normalization Options:

-c, --chromosomes str

A comma-separated list of chromosome names to include fends from when calculating correction parameter values. [all chromosomes]

-o, --output FILE

An optional filename to save the updated HiFive project to, leaving the original unchanged. [None]

HiC Complete Options:

-o, --output FILES

A set of three filenames separated by spaces to save the newly-created HiFive fend, dataset, and project files to. Mutually exclusive with -P/–prefix.

-P, --prefix str

A prefix for the output filenames. The file extensions .fends, .hcd, and .hcp will be used for the fragment, dataset, and project files, respectively. This option is mutually exclusive with -o/–output.

The maximum number of iterations to run the learning process for. [1000]

-t, --learning-threshold dec

The maximum change in log-likelihood necessary to stop the learning process early. [1.0]

-y, --binning-reads str

Which set of reads to use for learning correction parameter values, cis, trans, or all. [cis]

-v, --model str

A comma-separated list of fend features to calculate corrections for. Acceptable features are len (length), distance, and any features loaded in the BED or FEND file used to create the HiFive fend file. [len,distance]

-s, --model-bins str

A comma-separated list of numbers of bins to partition fend features into for modeling. [20,20]

-u, --parameter-types str

A comma-separated list of model parameter types. Acceptable values are even, fixed, even-const, and fixed-const. Even means that fend features are partitioned such that each bin has approximately even numbers of fends. Fixed means that the range of the feature is divided into fixed-width bins. The -const suffix indicates that the correction values are held at their seed-values and not updated. [even,fixed-const]

--pseudocounts int

The number of pseudo-counts to add to each bin prior to seeding and learning normalization values. [None]

The format of the output heatmap. Valid options are hdf5, txt, and npz. [hdf5]

-M, --matrix

Store output as a tab-separated matrix of values.

-y, --dynamically-bin

Dynamically bin heatmap.

-x, --expansion-binsize int

The size of bins, in base pairs, to group data into for expanding under-populated bins. [10000]

-f, --minobservations int

The minimum number of observed reads in a bin for it to be considered valid. [20]

-a, --search-distance int

The furthest distance from the bin minpoint to expand bounds. If set to zero, there is no limit on expansion distance. [0]

-v, --remove-failed

If a non-zero ‘search-distance’ is given, it is possible for a bin not to meet the ‘minobservations’ criteria before stopping looking. If this occurs and ‘remove-failed’ is set, the observed and expected values for that bin are zero.

HiC Interval Options:

-c, --chromosome str

The chromosome to pull data from.

-b, --binsize int

The width of bins (in basepairs) to partition data into. A value of zero indicates that each bin is to correspond with a single fend.

-s, --start int

The first coordinate of the chromosome to pull data from. None indicates the beginning of the chromosome. [None]

-e, --stop int

The last coordinate + 1 of the chromosome to pull data from. None indicates the end of the chromosome. [None]

-m, --max-distance int

The largest interaction distance to include in the interval file. A value of zero indicates no upper limit. [0]

The size of bins, in base pairs, to group data into for expanding under-populated bins. [10000]

-f, --minobservations int

The minimum number of observed reads in a bin for it to be considered valid. [20]

-a, --search-distance int

The furthest distance from the bin minpoint to expand bounds. If set to zero, there is no limit on expansion distance. [0]

-v, --remove-failed

If a non-zero ‘search-distance’ is given, it is possible for a bin not to meet the ‘minobservations’ criteria before stopping looking. If this occurs and ‘remove-failed’ is set, the observed and expected values for that bin are zero.

HiC Plotting Options:

-i, --image FILE

Generate an image from the region or regions for which heatmap data is being calculated. [None]

-p, --pdf

Format the image as a pdf. [None]

-r, --rotate

Rotate the image 45 degrees so the chromosome axis is horizontal and only plot the triangle above this axis.

-t, --ticks

Add coordinate ticks and labels to heatmap. This option can only be used if a pdf is requested.

-l, --legend

Add a color scale bar corresponding to interaction strength. This option can only be used if a pdf is requested.

-n, --names

Add chromosome names to the plot. This option can only be used if a pdf is requested.

-k, --keyword str

Pass additional plotting options accepted by the plotting module. Arguments should be of the format KEYWORD=VALUE. This option can be passed multiple times. [None]

HiC Multi-Resolution Heatmap Options:

-t, --trans

Calculate and include trans interactions in heatmaps.

-c, --chromosomes str

A comma-separated list if chromosome names to include in the heatmaps. [all chromosomes]

-f, --minobservations int

The minimum number of observed reads in a bin for it to be considered valid. [20]

-B, --maximum-binsize int

The largest sized bin to use (minimum resolution) in, base pairs. [1280000]